Sapporo Breweries Ltd. filed a protest over national tax authorities' earlier decision to refuse the brewery's request for a tax refund.
The beer maker lodged the protest with regional tax authorities in four prefectures and Hokkaido.
The authorities rejected in April refunding ¥11.5 billion ($93.7 million) that Sapporo claimed to have overpaid over revamping its beer-like drink Goku Zero last year, although they did not reveal the reason for the decision.
Japan's fourth-biggest brewery had voluntarily paid the money in additional liquor tax after the authorities requested last June data on the production of Goku Zero, which was then classified as a third-category beer, a drink taxed at lower rates than regular beers.
Sapporo relaunched the product as "happoshu" low-malt beer, which carries a higher tax rate than third-category beer. The ¥11.5 billion represents the difference between the two categories.
But the company later verified the product as third-category beer on its own and requested the refund in January. Sapporo continued to sell it as a third-category product for about a year.